Description

PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.

How to Use

To easily access the polyphen-2 executables, set your PATH using environment modules:

module load polyphen-2

Create an input file containing the accession code, the amino acid position, the wild-type amino acid, and the mutated amino acid, separated by tabs. Here is the example file /usr/local/polyphen-2/sets/test.input

P18887  399     R       Q
P18074  751     K       Q
P01023  1000    I       V
Q9BUG6  186     L       V
P15848  358     V       M
Q9UNQ9  110     V       I
P35568  158     P       R
P06241  445     I       F
P11245  286     G       E
P12259  1764    V       M
P51168  594     T       M
P16581  575     L       F
P08908  273     G       D
Q92889  706     I       T
Q92889  875     E       G
O75360  142     A       T
P11532  557     I       T
P00451  1260    D       E

At the command line, type

[helix]$ module load polyphen-2
[helix]$ cp $PPH/sets/test.input .
[helix]$ pph -d ~/polyphen2/scratch test.input > test.output

The option -d creates a directory tree to store aligments and profiles. You must supply a dumpdir in a shared area (either /home or /data) using the -d option.

The default database is UniRef100. The accessions shown above are from this database.

Documentation

• PolyPhen-2 Wiki
• Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010).